plotTSNE

Analysis

## Loading required package: plyr

## 
## Attaching package: 'igraph'

## The following objects are masked from 'package:flowCore':
## 
##     normalize, parent, tree

## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum

## The following object is masked from 'package:base':
## 
##     union

##     Compensation is applied on  ~/temp/fcs/2016-05-20_PANEL 2_ZF_panel 2_F1632217_009.fcs

## Run Rphenograph starts:
##   -Input data of 43333 rows and 9 columns
##   -k is set to 11

##   Finding nearest neighbors...DONE ~ 9.043 s
##   Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 2.074 s
##   Build undirected graph from the weighted links...DONE ~ 1.118 s
##   Run louvain clustering on the graph ...DONE ~ 1.272 s

## Run Rphenograph DONE, totally takes 13.507s.

##   Return a community class
##   -Modularity value: 0.8305925 
##   -Number of clusters: 30  Runing t-SNE...with seed 42  DONE

Starting from PBMCs, I think

TSNE results

TSNE results, colored by Phenograph clusters detected

TSNE results, colored by manual gates

TSNE results, Manually gated

Starting from Dendritic cells,Natural killer cells, Monocytes, I think

TSNE results

TSNE results, colored by Phenograph clusters detected

TSNE results, colored by manual gates

TSNE results, Manually gated